This repository contains the source code for our paper:
Z-upscaling: Optical Flow Guided Frame Interpolation for Isotropic Reconstruction of 3D EM Volumes
Fisseha A. Ferede, Ali Khalighifar, Jaison John, Krishnan Venkataraman, Khaled Khairy
--pattern represents a path where 3D image volumes in .tiff format and/or sub-directories containing z-slices of a given volume in a sorted order are located.
--model_path a path where the model used for evaluation is located (Download pretrained models Saved models).
--outputfile a path where the upsampled volumes will be saved.
--times_to_interpolate isotropizing factor by which the volume input is upscaled. If it's in 2^n order, it invokes recursive spatial interpolation to achieve the target number of frames, if not it will invoke the interpolation to the nearest 2^n order and apply bicubic interpolation to upsample or downsample.
--output_volume if true, isotropized volume will be saved in .tiff format.
--remove_sliced_volumes if true, removes the intermediate 2D slices generated from a 3D .tiff volume input.
python3 /Z-upscaling-main/eval/interpolator_cli.py \
--pattern "/Z-upscaling-main/Demo/*" \
--model_path /Z-upscaling-main/ModelPaths/test_run_ft_em_/saved_model_2M \
--outputfile /Z-upscaling-main/Demo_out \
--times_to_interpolate 8 \
--output_volume "True" \
--remove_sliced_volumes "False"